Stargate Atlantis: Mind's Eye
by the morrighan
Summary: This series of 12 stories is my spin on a Season Six of SGA.
1. Chapter 1

Stargate Atlantis: Mind's Eye

"Sheppard! Sheppard, we're dropping out of hyperspace in three, two what the…" Rodney McKay's stern voice rose in alarm as the city of Atlantis was violently jolted. As the towering city-ship dropped into real space it spun, shaking like a toy in a giant's hand. Rodney swore, grabbing onto a console as people fell around him, shouting and exclaiming. The lights flickered. Alarms whined. People were righting themselves and Radek Zelenka was muttering in Czech as he accessed a computer.

"Sensors are off-line," the Czech physicist informed calmly.

"What the hell was that?" Richard Woolsey demanded as he clung to a console. The city veered sideways before righting itself with a jolt.

Rodney ignored him. "Sheppard! Some kind of shockwave hit us! The readings are off the chart when I can get them! Can you—"

"Gee, really? I hadn't noticed!" replied the military commander's acerbic voice.

John Sheppard was prone in the Ancient Chair, sequestered in the bowels of the city. His palms were pressed to the arm pads as he guided the massive ship through space. Utilizing the star drives and his powerful ATA gene the military commander was locked in a strangely intimate connection with the city. He had been flying the massive vehicle back home. Back to the Pegasus Galaxy after saving the Earth from the threat of a Wraith attack.

John's mind was full of images and emotions as the city spoke to him and he spoke back, directing the ship where he wanted it to go. Directing it where the city wanted to go, if truth be told. It was almost like a sentient being, and John had learned very quickly how to communicate with it and at the same time have the ship obey him. So far the trip had been smooth sailing, as he would exchange places with Carson Beckett and the doctor could fly the ship while John got some much needed R&R.

Except now the shockwave had interrupted the smooth connection between man and machine and had sent both reeling.

Beads of sweat trickled along John's brow and down his neck as he closed his eyes, concentrating as he tried to reestablish the connection. He flexed his fingers in a vain attempt to grab at the controls, but there were none. Wobbling like a top the city stalled, shields flicking dangerously and threatening to expose the entire population to the cold, raw vacuum of space.

"Sheppard! Bring it under control now!" Rodney ordered, moving between two consoles and typing on two keyboards like some demented writer. "I can only partially access systems here!"

"I'm trying!" John rasped. "Damn it!" John licked his lips, wishing for a beer but instead forcing himself to relax and get the ship back under his control. A rumbling could be heard under him and John wondered if a star drive was about to explode.

"Do you need Beckett to take over?"

"No! I'm fine. Just give me a minute! How off-course are we?" he snapped.

Rodney jumped to a third monitor, shoving aside a hapless technician. "Only by a few kilometers. A few hundred…or so, that is," he clarified. "I'm sending the course corrections now…but whatever you do don't go left because the sun is that way and as you well know I burn very easily."

"Got it. No going left unless we want a tan," John said. "Acknowledged."

"Have you located our planet yet?" Richard asked, regaining his composure as the city was flying more or less smoothly now. At least it was upright again, although bumping along like a roller coaster at times. Richard hated roller coasters.

"Yes. We're not far…not too far," Rodney muttered, but he appeared worried. Data was still sporadically flashing on and off the screens.

"What was that? An attack?"

"No. Sensors indicate it was something at the very edge of the galaxy. Maybe weeks, or even a month ago and we are only feeling the effects now," Radek answered. "There are no enemy ships in the area."

"An exploding star or collapsing black hole or a planetary impact event," Rodney theorized, pausing to consider the question. "I will need more data to determine exactly what the—"

"Later, McKay! Let's get this bird down first!" John interrupted, before the scientist could be distracted by the astronomical mystery instead of focusing on the problem at hand. "I've got her under control but we need to break atmosphere ASAP! There's a fault in one of the star drives and it won't hold out forever!"

"Acknowledged," Richard said. He wiped his brow, moving between three screens and skimming over the scrolling data on each screen. Most of it was incomprehensible to him. "As soon as we safely land I want you to scan for the origin of whatever that was. And I'll need a complete inventory of our ZPM output." He turned as Teyla Emmagan approached with concern on her pretty face and a fussing baby boy in her arms. "Once we've landed we'll have debrief on our next move. We need to reestablish our off-world contacts."

"I wish to contact my people as soon as possible," Teyla agreed.

"Of course. We will need all the intel we can get."

"How long have we been gone?" Ronon Dex asked, joining the group.

"Two weeks."

"No, more like two months," Rodney corrected. He looked up to see everyone staring at him. Even Teyla's son Torren was staring as if in surprise. Rodney shrugged. "Time is relative. The hyperspace window sped up our time but not time here. It passed normally while we were moving much, much faster in the matter stream not to mention the distance between our two galaxies plus the quantum…oh never mind." He eyed a monitor. "All systems are active. Sheppard, take her in."

"Acknowledged," John said. He shifted on the Chair, relaxing into the odd communion of man and machine. He was flying the ship with thought instead of physical controls, and although he had flown the much smaller Puddle Jumpers flying the entire city of Atlantis was quite different and challenging. And exhausting. John had never felt so tired in his life, not only physically but mentally. He had to maintain a sharp mental focus at all times while monitoring the ship's massive drives, trajectory, shielding and a hundred different things with mere thought.

The city tilted then sped towards a planet composed mostly of water. It was a blue sapphire ball amid the blackness of space, and John aimed straight for it. John flexed his fingers again, slowing the city to an almost leisurely approach. They broke atmosphere and a chorus of alarms began to blare. The lights flickered again and John found himself having to argue with the city to get it to slow down its descent.

"John, we're coming in too fast!" Rodney declared.

"I know! Hang on! She's a bit eager to land!"

"She's eager? What?" Rodney shook his head, exchanged a look with Richard who merely shrugged. Pilot lingo was impenetrable to both men.

"Yeah, hang on!" John gritted his teeth, shifting on the Chair again, fingers stroking the pads now as it trying to settle a wild horse. "Easy, baby, easy…nice and easy now, baby," he muttered. The city seemed to hum in John's ears, as if responding to his tone, his touch, or if it recognized that at last it was home where it belonged. The ship slowed, slowed, gently rocked as it descended through the clouds, a softly spinning disc in the sky.

With an almost gentle splash Atlantis hit the ocean's surface.

And subsequently began to sink.

"Crap! No, no no baby, what the hell is this now?" John muttered, gritting his teeth and trying to visualize the star drive systems. Trying to shut them down one by one and integrate the city's buoyancy with the stabilizing anchors. Trying to cajole the city to do what he wanted and how he wanted it.

"John, we're sinking!"

"I know, Rodney! Just hold on, will ya? She's a bit temperamental."

"She's a bit? I'm a bit! I can't get the lock down procedure there's too much interference and whoa!" The city tilted wildly, sending people flying again as it was nearly upending in the water, effectively sinking sideways.

Abruptly the city lurched and righted itself. As if setting its feet down several sections lowered and anchored themselves onto the ocean floor, keeping the city in place. An audible groaning commenced then fell silent.

"Setting locks into place," John said stiffly. Sweat was beading on his brow again, and his muscles were tensing, holding him rigid in the chair as if he was actually physically moving the ponderous machinery. "Grounding stations are …wow." The last word was an exhalation.

"Wow? What wow? Is there a problem?" Rodney asked.

"No….just wow. The…never mind." John regretted his quiet exclamation. He couldn't begin to describe the way the city was responding to him, was purring under his mind like a cat as he stroked the pads and relaxed into the confines of the Chair, tension gone suddenly. The city seemed to enfold him in its mechanical embrace, returning the favor as a warmth flooded John's extremities and calm soothed his mind.

He briefly wondered if this could be considered as sex, and he snorted in amusement at the thought.

"We're secure," Rodney announced, breathing a sigh of relief.

"Lower the shield. Sheppard, you did it!" Richard smiled. "We will need a full systems analysis and a full assessment of our current power levels and what we will require in the future."

"Not to mention when we contact Earth…or if," Radek noted. He removed his glasses and wiped them clean on his blue shirt.

"We'll cross that bridge when we come to it," Richard decided, but the same worry filled his mind.

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John opened his eyes. At a thought the Chair righted itself from its reclining posture. John flexed his arms, moving to swing his legs over the side of the Chair. His clothes stuck to his back as he moved awkwardly to his feet. He staggered. He was abruptly dizzy and thirsty. As if now that the connection was severed he suddenly could feel every ache, every jolt, every need as he had been flying the ship for twelve straight hours and although he had the strongest ATA gene in the city he was still a human and not an Ancient.

He would have fallen had a hand not grabbed his arm and helped him remain standing.

"Easy, colonel, there you go." Carson Beckett steadied the other man. "You need to rest and replenish. Here."

"Thanks, Carson," John rasped, taking the proffered water bottle. He drank greedily, sloppily as water dribbled down his chin and onto his black clothes. He paused, frowning. "Water?" he asked, if only just realizing what the beverage was now that half of it was gone.

Carson smiled at his disappointment. "Yes, for now, John."

John scowled, but drank the rest of it. "I'm okay." He tapped his earpiece. "Woolsey, when?"

Richard's voice sounded tired, but calm. "The meeting? An hour, John. Get some rest first. We are stabilizing all systems and seeing to any damages."

"Be sure to eat something first, John," Carson advised, his Scottish voice full of concern. "I remember when I was flying this thing I became extremely peckish."

"Yeah, whatever. Okay. Thanks, doc. I could really use a cheeseburger."


	2. Chapter 2

Stargate Atlantis: Mind's Eye2

After a shower and a beer and a burger John felt more like himself instead of just an adjunct to the city. In some ways the city was almost sentient, and he pondered this as he sauntered into the conference room. He couldn't quite put it into words, this suddenly more intense connection he felt to the city. While he had been flying it the city almost seemed to sense his moods, and respond to them. Likewise he responded in kind, and it greatly helped him navigate the ship to where he wanted it to go. At one point he had been so completely immersed in flying the ship the city felt like an extension of him as if his arms and legs had been subsumed into the infrastructure of the buildings. It was both exhilarating and disturbing.

John shook off the thoughts, the worries, and the suspicions as he moved to an empty seat. Everyone was there, expressions ranging from serious to speculative. Teyla appeared the most peaceful, like she always did. Rodney appeared the most anxious, like he always did. Some things at least hadn't changed. John took a seat, smirking as Rodney was busy devouring a handful of popcorn.

"Oh. About time," Rodney complained through a mouthful of kernels. "We can finally start now." He brushed scattered popcorn pieces off his blue shirt.

John smiled irritably and clasped his hands together on the table, fingers interlacing. "If you're done eating, that is."

"How are you feeling, colonel?" Richard asked, ignoring the sarcastic banter between the two friends.

"Fine."

"Power levels have returned to normal," Rodney began without preamble. He reluctantly set his bag of popcorn aside, waiting a moment but John offered no other comments. "Despite the unexpected shockwave we managed to sustain only minimal damage, and the landing was a bit rough but we are still in one piece. All systems are mainly operational, and we are secured to the ocean floor but—"

"I knew there was a but coming," John laconically noted, causing Teyla to smile.

Rodney ignored him. "The substantial power drain of the city during its flight back and forth between galaxies has seriously undermined the efficacy of the ZPMs and our own Drones are depleted and the taxing use of the shield, although necessary has led to the near depletion of one ZPM entirely and the—"

"Get to the point, doctor," Richard nudged tiredly.

"I am," Rodney snapped, undeterred, but a look from Jennifer Keller made him swallow his ire. "We will have to temporarily shut down all extraneous systems while the power reboots, and I can replenish the ZPMs with the interfaces we took from Earth. I don't think I will have to initiate a full system shut-down but it is a remote possibility."

"I thought you said the city was fine," Ronon reminded, shaking his head.

"It is. We just need to—"

"Do what needs to be done," Richard decided, interrupting before Rodney could launch into another long discourse of explanations. "Is the 'Gate operational?"

"Yes, I was just getting to that. We can only—"

"We need to contact our off-world allies," Richard interrupted again, gaining a scowl from the physicist. "Teyla, I'm sure you would be willing to lead a delegation to your people."

"Yes, of course," Teyla agreed with a graceful inclination of her head.

"Wait, lead?" asked John, raising a brow.

"Yes, colonel. We need you here to organize our marines and set up new rosters and to help stabilize the city, should you help be needed. I'm told your particularly strong ATA might be necessary to initiate any flagging systems."

"There's a really good joke there somewhere," Evan Lorne muttered.

"And I don't want to hear it," John remarked, eying his second in command.

"I have a question," Carson ventured. "What about Todd?"

"What do you think we should do with him?" Jennifer squeaked.

"Kill him," Ronon stated.

"No. He's proven useful," John refused. He met the Satedan's gaze. Ronon appeared unconvinced and scowled, clearing wanting to end the Wraith's life as quickly as possible, but willing to defer to John's decision. For now.

"We let him go," Evan suggested. "We can use his ties to the Wraith Hive to gather necessary intel and then—"

"No."

"Excuse me?" Rodney challenged at John's stern tone. "If you ask me we should get rid of him. He's a liability now."

"I didn't ask you," John observed. "We keep him here until we learn exactly what the situation is out there. Then we can determine his usefulness as a hostage."

"And whether we still need him or not?" Evan asked.

"Exactly."

"And how are supposed to feed him? I don't see a line of volunteers, do you?" Carson challenged, clearly disliking having a Wraith in the city as well.

"I don't like having him around," Ronon said grimly.

"Nor do I, not with my son in the same city," Teyla agreed.

"I don't think I can gather any more information from him about the Wraith and their biology," Jennifer piped in, her high voice whining like nails on chalkboard.

"For the record the city doesn't like it either but for now it's our best option," John remarked. "He could be a useful bargaining too and then the..." he paused, as everyone was staring at him with bafflement. "What?"

"The city has an opinion?" Evan asked the question everyone was thinking.

"Never mind," John muttered, regretting what he had let slip. He shifted awkwardly in his chair, foot tapping on the floor.

"No, he's right," Carson interjected, blue eyes thoughtful. "I know exactly what John is talking about. It's the oddest sensation and I'm sure in your particular case it was much stronger than in mine. I have a few theories about the ATA and how it interacts with the very functioning of the city, not only the systems but the—"

"Drop it, doc," John warned, abruptly uncomfortable.

"What the heck is he talking about?" Rodney asked, looking from one to the other. "It's just a machine, essentially, a very advanced machine but still a—"

"It's more than that, isn't it John? There is something intangible but it is there, a—"

"I said drop it, doc!" John insisted, his voice rasping a little forcefully. He forced himself to relax and sat back in his chair. He couldn't explain why he was so defensive, as tension coiled in his frame. He swallowed. "When you do think the flak from Earth will hit?" he asked, steering the conversation in another direction.

"As soon as we establish communication with—"

"That was it!" Rodney exclaimed, slamming his hand on the table as Richard eyed him. Stray popcorn kernels jumped. "We can't! We do not have the power to even attempt radio communication with Earth at the moment, and I fear it will be some time before we can try. The power requirements are just too great while the city repairs itself and we get all systems back to full power."

"Then that's a good thing," Ronon noted.

"Yes, it is," Richard agreed. "It may give them time to cool off after our sudden departure. I don't think they will be very pleased with us."

"That's the understatement of the year," John commented wryly.

"What else could we do?" Rodney challenged. "They all wanted a piece of us! The IOA, The NID, the CIA, even the SGC couldn't wait to break us apart and divvy us up!" he fumed, clearly outraged. "They would have torn us apart and bickered for years over who had the right to control this city! Our city! My city! And no one understands this city better than us! Than me! They have no right to our city! They wouldn't even begin to understand it!"

"Yes, Rodney, we know. The—" Richard began, but Rodney moved to his feet, impassioned.

"No, you don't know, Richard, you don't know the extent of their haggling over us! They would have broken us up! They would have sent me to Area 51 and John to God knows where on some stupid SGA mission and Carson to NORAD and Ronon and Teyla would have been stranded and no doubt imprisoned because they are aliens now aren't they? They would have torn apart this city piece by piece to try to understand how it works and in the end they would have destroyed it by their pointless and childish bickering over ownership of it!" He paused. He cleared his throat and resumed his seat, embarrassed. "I'm just glad we came back here, is all I am saying."

"That's why we ran away," Evan noted with a smile.

"Flew away, actually," Carson clarified.

"It's called a tactical retreat," John corrected.

"Will there be repercussions?"

Richard nodded as Teyla's question sobered the room again. "I am afraid it is unavoidable. But it is nothing we can't handle. That I can't handle," he added, as if relishing the challenge of any debate over ownership of Atlantis. "It's not like we're just around the corner any more, is it? We are safely out of their clutches and they know it. And they know we know it."

"We have superior weapons," Ronon said.

"What? No, it won't come to anything like that," Richard assured. "It's all a political battle now. It's a battle of words and backroom dealings and negotiations and bribery."

"Which leaves us where, exactly?" Carson asked.

"Here." All eyes moved to John again. He straightened in his chair, abruptly serious. "Right here is where we belong, where the city has always belonged, in the Pegasus galaxy. Rodney's right. We never belonged on Earth where they would bicker over us for years, even centuries, probably, locked in boring meetings and political shenanigans and memos that would make boring reading. As soon as we can we will resume missions. We need a layout of the land, so to speak. Rodney, you said we've been gone for two months?"

"More like three," Rodney admitted, pleased that John had endorsed his views. "Time bends differently within the hyperspace wormholes and between galaxies and the—"

"Whatever," John cut off the scientific babble with a shrug. "Things can't have changed that much in such a short time, can they?"


	3. Chapter 3

Stargate Atlantis: Mind's Eye3

"Whoa, whoa!" John held up his hands as weapons of all kinds were pointed at him and his team. The first trip through the Gate had resulted in a sudden display of blatant hostility before they had even reached the village. People had surrounded the team, raising weapons and not letting them get far from the Stargate, which was a good thing, considering their reception. "Take it easy now! We know you guys and you know us. We're allies, remember?"

"No longer," a man said. The contempt in his voice was obvious. It was on the face of every man and every woman facing them.

John glanced at Ronon and shook his head. The Satedan reluctantly lowered his big gun but kept it out at his side. Rodney has lowered his after a moment, appearing stunned by their hostile reception. Although boring these people were normally very friendly and eager to trade.

"We are from Atlantis. Do you not remember?" Teyla asked, holding her own weapon at her side. Unable to make a connection to New Athosia the team had opted for this planet, a pleasant world of blue skies and ripe fields, but now Teyla was regretting their choice.

"Oh, we remember you, all right," the man agreed, but his tone conveyed hostility.

"Atlantis," one spat the word out as if it was vile. As if it were something foul to be expurgated and cast aside like garbage.

Rodney blinked, as startled by the reaction as his friends were. "I don't think we're very welcome here, John."

"Gee, Rodney, ya think? What the hell is going on here?" John demanded. His fingers tightened on his P90, just in case. Like most worlds the indigenous population was no match for their superior weapons, however outnumbered. Sometimes a show of force was necessary.

"Your friend is correct. You are no longer welcome here." A woman stated. She was glaring at the team, clasping a sword in her hand so tightly the whites of her knuckles showed.

"I do not understand. We have always been friends with your people," Teyla reasoned, taking a step forward but a look from John stilled her. "We have often traded successfully for our mutual benefit."

"No longer. You left us to our fate and only the Coalition saved us when the Wraith united," the man informed.

"Whoa, what? The Wraith united? When did that happen?" John asked. He glanced at Teyla and Ronon. Their shock mirrored his at this unexpected revelation.

"The Coalition? Is that still trying to run the galaxy?" Rodney asked. He remembered the loose alliances of several planets. He remembered when that Coalition had put Atlantis on trial, his team on trial, him on trial for perceived wrongs. Only Richard Woolsey's quick thinking had gotten them out of that one. It looked like some more quick thinking was in order. "We are allies with the Coalition."

"Look, we had to leave to defend our home world against the Wraith, but now we are back and can assist you with whatever—"

"You are no longer trustworthy and no longer welcome here. Go!" Guns and swords bristled. The crowd advanced, as if to corner the team or herd them back towards the Stargate as quickly as possible.

John gestured and Ronon lifted his gun as John hefted his P90. All it would take was one loose trigger finger or eager swing of a sword and all hell would break loose. John was determined not to be caught in any crossfire, from either side. "Fine. If that's how you want it we'll go. Peacefully. Rodney, go dial the 'Gate."

"I never liked this planet anyway," Rodney commented, moving to the DHD and dialing Atlantis. "There were too many harvest festivals and too many agrarian settlements and the lack of even basic sanitation, mind you was a deterrent not to mention the overabundance of citrus and the…" he babbled nervously as his he pressed the necessary symbols.

"When did the Wraith unite? How did they unite?" John asked, slowly removing his sunglasses with his free hand. But the aspect of the villagers remained the same without the aviator's kinder lens to block the blistering sunshine.

"That is of no concern to you. We are under the protection of the Coalition now."

"How may we get in touch with this Coalition?" Teyla asked, attempting a different tactic. Her open hands were at her sides as she had placed her gun in her holster.

"That is not for me to say."

"Wonderful," John noted. Contempt laced the one word. With a smooth motion he restored the sunglasses to his face.

"Let's go, Sheppard. They don't want our help," Ronon said, equally disdainful. If they were no longer welcome here there were a dozen other worlds which would gladly receive them.

"Even if you no longer trust us we can still be allies against the Wraith," Teyla reasoned. "Please tell us what has happened during our absence."

"I would rather die than help one such as you."

"That can be arranged," Ronon growled, then smiled. He gestured with his big gun.

"I do not understand," Teyla persisted.

"Him I understand." The man gestured at John. "He says he left to defend his people. But you, Teyla Emmagan, abandoned yours long ago."

"What? I never—"

"This is pointless," John decided, interrupting her outraged shock. "Let's go. Rodney?"

"Sending the IDC now," the physicist informed, glancing over his shoulder to see weapons were still trained on his teammates. The wormhole could not open fast enough. He kept glancing over his shoulder lest a stray arrow strike him in his back, or lower, as had happened before to his everlasting regret. He still had a scar from that experience.

"Wait. I do not understand. I never abandoned my people!" Teyla insisted, upset at the accusation. She took another step forward but the weapons trained on her made her stop.

"You abandoned them and now you are no longer welcome here either. Go now, or we will make you leave by force!" The crowd began to move forward as one, but John fired into the air, startling them.

The potential for violence was only a breath away, and all knew it. John slowly, so slowly lowered his weapon, sweeping it along the air as if he would mow down the insurgents but merely demonstrating how easily he could. The feeling came and went in the blink of an eye.

"We're going. Come on, Teyla. We'll get to the bottom of this," John urged, taking her arm and guiding her towards the shimmering wormhole as he walked backwards, gaze locked on the villagers. The crowd was watching, all grim-faced. "Oh. And thanks for the hospitality."

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Evan shook his head. Shook it again, disbelief on his face. "It's like I said, Mr. Woolsey. Dead. There's not a soul on P1R279. Every man, woman, and child were either culled or killed and left to rot. There's nothing left alive on that planet." He repressed a shudder at the carnage his team had encountered. Bodies strewn in grotesque postures where they had fallen, killed by stun blasts or large knives or weapons that he couldn't even identify.

Richard frowned, glancing at his data pad, back to Evan and his haggard-looking team of marines. According to his report this planet had a thriving population and was expanding into more towns. "And you searched a few villages?"

"Yes sir. Several, in fact, but all we found were dead bodies, or no bodies. To be honest I don't know what happened out there, but it wasn't pretty."

"And you encountered no resistance? No Wraith in the area?" John asked.

"None, sir. Whatever happened there must have been weeks ago, judging by the decomposition of the bodies." Evan made a face at the memory. "We filmed a few for Beckett to examine, but I don't think he'll find anything except what we did."

"It doesn't sound like an ordinary culling," John mused, rubbing his chin. "They wouldn't deplete their food source like that. Would they?"

"According to Doctors O'Meara and Beckett, no," Richard remarked, frowning. "Unless the attack was in retaliation for some perceived wrong. Perhaps they discovered an enclave of Hoffan serum survivors. A united Wraith front is a terrifying prospect. But I am more disturbed by this sudden vehemence against us. Any theories?"

"Plenty but no facts. Yet. We're going to reconnoiter a few more worlds and see if we can get any intel," John decided. "At least those that we can dial successfully, that is."

"We need to get in touch with this Coalition. I'm surprised they haven't attempted contact with us yet, actually."

John stood. "First I need to talk to Todd. For now missions are restricted to military personnel only, until we learn the extent of this dissidence."

"Dissidence? We were hardly their rulers, John," Richard noted.

"Weren't we? If they think they can fight the Wraith on their own then good luck to them." John paused, shaking off the odd thought, the odd feeling. "Something's very wrong here and I have a suspicion about who is fueling all of this anti-Atlantis sentiment. Lorne, check out M7G-677, the kid planet."

"Yes sir. I don't think they would have turned against us."

"Just be cautious, major, in case they have. Dismissed." Once Evan and his team had gone John turned to Richard. "I want new protocols for missions put in place until we learn more. I'll get on citywide and pull the team leaders into a meeting to activate them. We'll put out some feelers towards the Coalition once we can establish a secure, isolated radio contact. Any luck with our power problems?"

Richard sighed. "Not yet. Maybe with Rodney here now we can make some headway. We still don't have sufficient power to even attempt dialing to Earth, and some addresses are still locked out of the data base. Are you sure about that? I mean about restricting the off-world teams?"

"Yes. Until we can be reasonably sure that we won't be attacked I don't want any civilians placed in harm's way. Except for my team, that is. But not Rodney. I think you need him here more than I need him out there."

"Agreed. Teyla will be anxious to go to New Athosia."

"Yes, and we will once we can get a lock on the address." John frowned. He moved to the doorway, turned back to see Richard watching him. "It's like…it's like the city doesn't want us to go to certain places." He touched the door frame.

"It is? And why would that be?"

"I don't know."

"Are you suggesting the city is making a conscious choice as to where we can and can't go."

"No. I mean obviously it's a power fluctuation issue, but still…" John couldn't describe the feeling. He shrugged. "Never mind. I'll need a list of what addresses can be dialed, and which ones can't right now. We can go from there."

"Radek's already on it," Richard said.

"In that case I need a drink before I talk to our resident Wraith," John noted, as he exited the conference room.


	4. Chapter 4

Stargate Atlantis: Mind's Eye4

Todd was pacing, pacing. He hated being held in a cell. He hated being in Atlantis. He hated being a prisoner. He hated being hungry. But the Wraith were a patient species. Living for centuries tended to alter one's outlook on time. Nevertheless Todd felt a very human impatience at being locked up like this and deprived of food and being with others of his kind.

Most of all he hated John Sheppard. Nevertheless he smiled as his nemesis approached, dismissing the two guards with a flick of his hand. The Wraith watched him, suspicious, alert. This human was at times unpredictable. "John Sheppard," he said in an oddly musical lilt that still managed to send a shiver up the man's spine. "Is this how you treat an ally?" His tone was almost scolding.

"No. This is how I treat you," John replied, coming to stand outside the cell. A blue force field glimmered between the sturdy bars. "I need information."

"And I need food. Within this cell I can provide you none!"

John stepped closer, clasping his hands behind his back. "Within that cell I can't provide for you either. Can you make contact with your kind?"

"Yes. But not from here." He gestured around the cell, elegant motions of his long fingers trailing the air. He stared. He tilted his head, his eyes turning to slits for a moment. "Something has changed."

"A lot has changed," John admitted. Finding it oddly easy to talk to his Wraith compared to some people he knew.

"And you wish for me to find out for you."

"Can you make contact or not?"

"I need sustenance first. Hmm?" Todd smiled, tilting his head again as if flirting.

John grimaced at the thought. "Sorry. Nothing here on the menu would suit you."

"Really? You've gotten around that before, John Sheppard. You convinced a man to offer himself to me."

"A guilty man volunteered to right a wrong and to save lives," John corrected, but he tensed. Todd's version was closer to the truth and both knew it.

"We both know what happened, John Sheppard," Todd intoned, as if reading his mind or his emotions. "About that. About this. You hold me here as a prisoner. What possible motive could I have to help you?"

"Freedom," John replied. "You give me what I need. I let you go."

"Truly?" Todd laughed. It was a discordant sound which was both very alien and very human at the same time. "Now who is being deceptive?"

"That's the deal. Unless you'd prefer to rot in this cell until you die of hunger. I've been led to understand that could take a very, very long time." Now John smiled, as if relishing the thought of seeing Todd slowly, slowly starve to death.

Todd glared. A flash of hatred and pure animal rage so deep that John almost took a step backwards away from the cell, although he was perfectly safe. A moment later and that mask of calm amusement returned to Todd's face.

John kept smiling. "I'll give you a day to consider it. Might help keep your mind off how hungry you are. If you'd like I could have Doctor Keller give you that treatment again. Oh…that almost killed you, didn't it? My bad." John turned and walked away from the cell, gesturing for the two guards to return.

Todd's glare remained.

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Teyla was busily bouncing Torren on her lap. The baby was fussing again, and nothing was soothing him. He rejected his pacifier. He rejected his bottle. He rejected his plush toy bear. "But why would he say such a thing to me?" she complained again. "I have never abandoned my people. Our people!"

Kanaan nodded, watching his wife try to pacify their son as he tried to pacify her. "I agree. Perhaps he spoke out of spite, or anger. You have nothing to worry about, Teyla."

"But I do! I need to get to New Athosia as soon as I can! I am concerned over the fate of our people. Now that I have learned we have been gone months instead of weeks they may have lost their faith in me, in Atlantis."

Kanaan smiled. "No one could ever lose faith in you, my love."

Teyla smiled at his affection, but her smile faded. "Has there been any progress on the 'Gate accepting the address?"

"Not yet. There seems to be some sort of internal locking mechanism in the dialing program. It is only affecting certain worlds, but it seems to be completely at random. Doctor Zelenka is running a simulacrum to see if he can find the glitch. What? You find this amusing?" he asked. Teyla was smiling again at him, her eyes full of humor and affection.

"No. I find it refreshing and wonderful that you have taken to the city so quickly. Look at you, Kaanan! You even wear the clothes of a Lantean now."

Kanaan smiled, glancing down at his Atlantis BDUs. They were drab, a simple gray t-shirt and navy pants, but they were serviceable. "Yes. I am merely a technician in training, but Doctor Zelenka says I have a knack for things mechanical. I must admit I find it quite fascinating and challenging. I think I prefer it to farming or hunting or even a harvest festival."

Teyla chuckled. "I am glad to hear it, Kanaan. And when Torren is old enough you can begin teaching him your new skills."

Kanaan grinned. "If he ever stops fussing, that is!"

As if in protest the baby started to wail.

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Rodney shook his head. "These readings don't make any sense!" he complained for the fifth time as he sat, hunched at a console in the control room. He had shooed away the technicians, angrily batting them away like flies as he scooted from console to console, from reading to reading, but the screens all projected the same data.

"We've been over this already," Radek Zelenka replied for the sixth time, sitting next to the Canadian when he was still, that is, and equally entailed in the search for solutions. The Czech adjusted his glasses and sighed, shrugged. "Between the power disruptions and the long-range scanners being off-line it will take more time to track anything."

"And we need to go over it again! That shockwave didn't just appear out of nowhere! If there's some kind of powerful new weapon out there we need to find it!"

"Are you so sure it was a weapon?"

"Yes! All right, no, but odds are that whatever that was it was not a naturally occurring event. I'm extrapolating backwards but the wave was massive and there is a lot of interference. It will be difficult to track back to the origin of the wave, given the time lag and the dispersion rates not to mention the interstellar traffic of the—"

"Leave that, Doctor McKay," Richard said as he joined the two arguing physicists. "It's more important that we have all systems operational in the city. I need every Gate address unlocked. More importantly we need all systems dealing with defense up and running."

"Defense? Are we under attack?" Rodney asked, looking round the serene confines of the control room, at the Stargate below where it stood, inactive, immovable. Everything and everyone seemed to be in their place. Even the bumbling technicians were where they should be, in his way as usual. With a sudden jolt the Stargate started to light up symbol by symbol. It was ponderous and noisy and that wasn't normal.

"Not yet. It's just a precaution. As you have discovered we apparently ruffled quite a few feathers by our absence." Richard glanced at the Stargate, seemingly unperturbed.

"I'll say!" Rodney agreed. "You should have seen those people! They looked like they were out for blood! As if we were the enemy and not their saviors! Without us they would have fallen to the Wraith long ago, and just look how they repay us!"

"Off-world activation!" Chuck Campbell announced, sitting at his monitor. "Receiving Major Lorne's IDC." He waited a moment, staring at his screen, waiting for the data to stream across his monitor and the encryption codes to unlock. "Authenticated."

"Lower the Shield," John said, joining them. "That didn't take long." He exchanged a look with Richard and sprinted down to the Gate room as Evan and his team emerged from the shimmering wormhole. Quick trips were never a good sign. "Major?"

Evan stepped away from the wormhole as it dissipated. His team moved with him. The marines appeared tired, spooked. They were clutching their weapons even though they were safely in Atlantis and among friends.

"What about the kids?" Rodney asked, suddenly joining them. "How were they?"

"Gone."

"What?" Rodney exclaimed. "That planet was protected by a ZPM-generated shield! Nothing could have gotten through it!"

Evan shrugged. "It must have failed. We had no trouble flying in and landing. The planet is deserted, sir," he continued, turning to his commanding officer. "There's no one there. What's worse, there's a Wraith outpost there now. There were several Wraith in the immediate vicinity but they were more interested in moving into their new digs than watching out for us. We escaped notice and made our way back home undetected."

"A Wraith…how? What the hell is going on?" Richard asked. "They don't do that, do they?" Richard looked round for confirmation. "I mean they don't settle on planets like that, right?" He wished there was a Wraith 101 manual for times like this.

"They never have before," Rodney said, "at least not on an inhabited planet. Well, only for a limited amount of time…or for, um, breeding Drones." He remembered the repulsive sight of the engorged queen birthing Drone warriors like so much larvae. He thought of all those children and young adults on that planet and felt a flash of despair over their fates.

"Or a crashed Cruiser," John added, as similar memories flashed in his mind. "Ordinarily they don't settle planets like that. They live on their Hive ships." He considered a moment. "There's only one way to find out." He frowned, deciding. "We need to contact Ladon Radim."

"The Genii? Are you crazy?" Rodney exclaimed.

"The colonel is right," Richard agreed. "It's time we stopped blundering around in the dark."


	5. Chapter 5

Stargate Atlantis: Mind's Eye5

John and Rodney were strolling down the hallway. Rodney was babbling on about some mathematical equations as he was consulting his ever-present laptop, talking a mile a minute. John was ignoring him, having more pressing concerns on his mind such as what to have for lunch. The two men veered to the left as a group of women were approaching on the right, a group of scientists judging by their BDUs and the white coats among them.

John smiled at them, making eye contact with each one as he slowed his steps, taking in the details of each woman as they returned his smile in turn, halting their own conversations to enjoy the brief but beguiling attentions of the military commander.

"There's no time for that," Rodney said suddenly, noticing John was now a few steps behind him. He waited for John to catch up to him.

"For what? I was just being polite."

"Sure you were. So I've been thinking."

John waited, but Rodney said nothing else. It was such an unusual occurrence that John stared at him. The two men made their way into the cafeteria and grabbed trays to fill with sandwiches and bottles of water. Still the physicist said nothing as they took a seat opposite each other at an empty table. Enjoying the sudden respite John bit into his turkey sandwich, chewing and swallowing. He drank some water. "And?" he reluctantly prompted at last.

Rodney set down his sandwich, still untouched. He stared at the heaping of meat and veggies between the two slices of bread. "The thing is…I've been thinking."

"So you said."

"And I just, well, you've been through this before and I'm not asking for advice or anything like that but maybe I am. I tried this once before and well I almost tried it once before but I never actually got there, to actually saying the words and all, you know, and I failed miserably. I thought I might ask you about how to approach it since you-"

"Spit it out!" John snapped, regretting he had encouraged his friend to talk.

"Would you marry me?"

John didn't blink. He didn't miss a beat. "Can I see the ring first?" he quipped.

"What? No! No no no no no not you! I didn't mean it like that! I meant as a woman. I mean I've tried this before and it didn't go too well. All right, it didn't go at all," Rodney spluttered, becoming more embarrassed as John just stared at him, "and I know it might be stupid, okay, it is stupid to try it again and you've been down this road before and yes, it didn't work out for you either, I realize that but at least you got there and made it past the proposal which I have yet to do." He took a breath at last.

John tried not to smile. "Rodney, relax."

"Relax? How can I possibly relax?" he fumed, but lowered his voice. "I know what you're thinking," he continued after taking another breath and releasing it, "and I'm thinking it too but we've been together for a while now and it seems to be working despite the fact that a woman like that is way way above me and yes I'm not worthy of her and she's so much—"

"You're going to propose to Keller?" John finally managed to interrupt.

"Yes! What do you think I've been talking about, the weather?" he flared, defensive.

John smiled. He stood. He stepped round the table, grabbing his sandwich and water. He placed his hand on Rodney's shoulder. "For the record I was thinking that girl isn't worthy of you, Rodney. That she'd be lucky to have you. But if that's what you want I say go for it. Good luck."

"I…huh?" Rodney found himself speechless, an astonishing thing in and of itself. He turned and stared after John as he strolled out of the cafeteria, munching on his sandwich. Rodney turned back to stare at his own uneaten food as if it had the answers.

It didn't.

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Richard frowned. He was staring over Chuck's shoulder, which irritated Chuck to no end but the technician said nothing. Richard stepped away at last, muttering to himself. "I don't like this. I don't like this at all."

"Is there a problem?" John asked, joining them as he demolished the last of his sandwich. He wiped his mouth with the back of his hand.

"No. Yes. The Manarians have agreed to broker a meeting between us and the Genii. I know they are not the most trustworthy group of people, and yes they betrayed us before to the Genii but at least with them we know exactly whom we are dealing with and they are sometime allies of the Genii. It seems the Genii won't talk to us unless it's on neutral ground and face to face."

"Sounds reasonable," John said after a moment. "What's the catch?"

"One representative. Alone. Unarmed."

"Unacceptable."

"We don't have a choice, colonel. You and I both know that the Genii have in all likelihood taken over the Coalition in our absence. We either work with them or—"

"Against them," John finished for him. "I'm fine with that."

"Until we know the bigger picture I want to keep our options open. So I am going."

"No. I should go. I've dealt with the Genii and Radim before this, and I can handle the duplicity of the Manarians."

"No, colonel," Richard refused. "I need you here to safeguard the city and to keep monitoring our off-world contacts. If it comes down to choosing sides we need to know who is on ours and who isn't. Safe passage has been assured."

John smiled, but it wasn't a pleasant smile. "Yeah, right. And the Manarians always keep their word, just like the Manarians."

"It's a risk we'll have to take. I'm sure they know what will happen if I don't return."

"Atlantis will bring all of its considerable force to bring you back," John agreed.

Richard smiled. "Yes, although I would have put it in less threatening language."

"I don't like it, but if that's your decision…" John frowned, realizing that Richard was right. That he had already made the choice judging by the fact that he had his briefcase next to him. As the leader of the Atlantis expedition he could make any and all decisions without consulting anyone, even the military commander. Still it annoyed John that the decision had already been made without being consulted and a flash of ire came and went.

"It is. If I don't return in two hours…" Richard left the rest unsaid. He trusted John to do the right thing for the city and its inhabitants. "Chet, dial it up, please."

"It's Chuck," Chuck sighed, but nevertheless dialed the address.

Richard took hold of his briefcase. His hand slid up to where his tie should have been, but he was wearing Atlantis BDUs and the uniform precluded the necessity of a tie. He walked down to the Stargate as the KAWOOSH filled the room with kinetic energy, then collapsed back on itself in a shimmering pool. "I've got my subcutaneous tracking device, of course, in case things don't go well, plus another one in my briefcase," he told John as the other man strolled beside him. "With any luck I can negotiate a truce if not an alliance against the Wraith."

"I'd feel better if you had a gun. Just be on your guard. Even with Radim in control I do not trust the Genii. Assuming he still is in control, of course. If you're not back in two hours I will initiate a search and rescue."

"Thank you, colonel. I leave the city in your capable hands." Richard strode into the event horizon.

John stared after him, watching the wormhole dissipate. He eyed the Stargate a moment as the lights flickered, flickered, in time to the sudden queasiness in his stomach. He returned to the control room, glancing at the monitors, at Radek who was muttering in Czech again which was never a good sign. "Problems?"

"The Stargate is taxing out the ZPM levels which should not be happening," Radek informed.

"That's odd. For a moment I lost secondary controls," Chuck noted, fingers pausing on the keyboard before resuming their dance of commands. "What could cause that?"

"I don't know." John tapped his earpiece. "McKay, what's going on with the city?"

Abruptly the power rose and fell and fluttered wildly, filling screens with nonsense and causing doors to open and close, open and close. An alarm blared, was silent. "McKay? What ow!" John rubbed his ear as a hiss of static blared from the comm unit. "Great, just great, what else can go wrong today?"

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"Sheppard!" came the irate voice of Rodney over the earpiece. "I need you down here now! Power levels are decreasing and the ZPM is failing! Ancient Chair room!"

"I noticed!" John replied, breaking into a run as the city abruptly went dark for a moment. He swerved to avoid running into some marines. Stopped. "Lorne! Get to the control room! Make certain the comms stay active!" he ordered.

"Yes, sir!" Evan broke into a run up the hallway.

"What the hell happened?" John asked, resuming his run. "Rodney!"

"That last 'Gate trip seems to have overloaded the systems! I can create an interface between our equipment and the ZPM but I need you to talk to the city and tell it what to do! I can't believe I just said that," he grumbled.

"Why the Chair?" John asked, quickly descending a flight of stairs. Lights flickered dully. An alarm was whining but it sounded weak, almost half-hearted. Doors were sluggishly closing, as if in response to some unknown threat.

"Because it's a primary system and can control the auxiliary systems at this level!" Rodney replied, on his hands and knees and working furiously to connect wires and crystals in a hodge-podge of circuitry. He balanced the flashlight in one hand. "I need your ATA to direct the power surges and damn it!" He withdrew his fingers as a sudden flare sent the power sparking in all directions.

"On my way! I need that 'Gate functioning!"

"Nothing will function if you don't get down here!"

The city went black. It went completely black as all power failed all at once. Even the emergency lights flickered and were dissolved into the blackness. All machines were silenced. Only the sound of bubbling water remained.

A hush fell over the city as it was consumed by shadows.

"Sir? Colonel Sheppard, we, um, we've got a situation, sir," came a nervous voice over the earpiece, interspersed with static.

John increased his stride. "A situation? What the hell does that mean, lieutenant?"

"Sir…um, it was so fast. We lost power and when we used our lights to—"

"Can the excuses and tell me what happened!" John ordered.

"Sir, its Todd. Todd's escaped."


End file.
